Download (4) QTLs to networks: eQTL analysis

(4) QTLs to networks: eQTL analysis
Chr 9
3.8 Lod
p >0.01
22.4% of variation
Lecture objectives
By the end of this lecture you should be able to explain:
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How QTL analysis/genetics has been fused with genomics
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What eQTL analysis can do compared to standard expression
analysis using microarrays
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What the different types of eQTLs are
• 
What the challenges associated with eQTL mapping are
What is expression QTL (eQTL) analysis?
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Recent development
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Classical QTL analyses combined with gene expression profiling
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Identify genomic locations that significantly influence the amount of
protein or RNA made by a particular gene (gene expression)
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Expression of each gene = a trait; genes affecting it = eQTLs
How does eQTL analysis differ from genomic analysis?
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Large-scale gene expression data from microarray experiments:
- information about regulatory relationships between genes
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Most approaches to transcriptional network inference rely on this alone
- based on external environment perturbations
- single-gene perturbations in homogeneous genetic background
eQTL overview
quantitative variation of mRNA
levels in a segregating
population
Expression QTLs
genetic determinants
of gene expression
Additional level of knowledge from eQTL analysis
QTL analysis
Association mapping
eQTL analysis
Gene
Gene
Gene
Gene
% of
effect
Phenotypic
trait
Phenotypic trait
% of
effect
270
% of
effect
% of
effect
270
% of
effect
Gene
% of
effect
Gene
Some things to consider with eQTL mapping analysis
• Identify & map genomic regions that significantly affect gene expression levels
- Statistical methods and power to map eQTLs
• 
Common design: use RILs and examine a number of microarrays across
a modest set of lines (10-100)
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Some improvement in power (over an F2 design) occurs because of
being able to replicate within each RIL and the expanded map distances
(4 fold) found in RILs vs. F2
• 
eQTL mapping faces many of the same lack of power issues as QTL mapping
Some issues with eQTL mapping analysis
• Identify & map genomic regions that significantly affect gene expression levels
- Measurement error/noise (could be high for microarrays)
- Justification of mapping procedures and therefore results
For markers: evaluate linkage statistics for each genetic marker and
use permutation testing to provide genome-wide corrected p-values
For microarrays: determine the expected proportion of false positives
called significant in the linkage analysis (FDR)
• Aim to identify cis-and trans-regulation of eQTLs
cis- and trans-acting eQTLs
• 
Used in a variety of species, including humans and rodents, to
help elucidate the molecular basis of complex disease
• 
Cis-acting eQTLs:
- caused by genomic sequence variants
that reside within or close to the gene
being regulated
- attractive candidate genes for
(patho)physiological QTLs (pQTLs)
mapped to the same location
Candidate genes
for physiological traits
cis- and trans-acting eQTLs
•  Trans-regulated eQTLs:
- reflect differences in remotely regulated gene expression and
- often occur in clusters: co-ordinated master regulation of many genes
• Master regulators of gene expression - key control points in gene networks
Regulatory gene networks
Expression
Identifying cis and trans gene regulation
Jansen & Nap (2001)
Trends in Genetics: 17, 388-391
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Gene 3 = not regulated in cis or by any other gene
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Gene 1 = only controlled by B = cis regulation
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Gene 2 = controlled by A = cis regulation & by gene 1 B = trans regulation
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Gene 5 = not cis (C) controlled
but controlled in trans by 1 B
& 2 A
& 3 F
Moving to eQTL networks
Expression
Constructing regulatory networks (hypothetical example)
Jansen & Nap (2001)
Trends in Genetics: 17, 388-391
• 
• 
• 
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(d) Expression level analysis
(e) Information about gene function
Gene 3 = not regulated in cis or by any other gene
Gene 1 = only controlled by B = cis regulation
Gene 2 = controlled by A = cis regulation &
Gene 5 = not cis C controlled
D
by gene 1 B = trans regulation
but controlled in trans by 1 B
& 2 A
& 3 F
&4
Challenges to eQTL mapping analysis
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Low levels of gene expression
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Fine mapping:
- Due to the spacing of genetic markers and/or linkage
disequilibrium, several genes can reside near each marker
- Identifying the true causative gene requires additional data,
since all genes at a locus are indistinguishable based
on the eQTL measurements alone
• 
Lack of mechanistic explanation:
- A gene-phenotype association = little insight into
underlying molecular mechanism for the association
Some ways to solve the problem of fine mapping
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Simple fine-mapping techniques
- linkage disequalibrium mapping
- additional genotyping of loci and individuals in regions of interest
• 
Main bioinformatic focus has been on predicting which genes within
a given locus are the true regulators of expression of the target
e.g. Kulp and Jagalur (2006) sought to infer the true causal genes
using a Bayesian network model constructed from expression correlations
detected within the eQTL profiles
More ways to solve the problem of fine mapping
• 
Complement eQTLs with data on physical molecular interactions
e.g. Tu et al (2006) modeled each eQTL association as a sequence of
transcriptional and protein–protein interactions (PPIs) that transmits
signals from the locus to the affected target
Integrating eQTL data with additional independent information
may significantly reduce the noise and improve the
statistical power of the analysis
e.g. a strategy to identify master transcriptional regulators
modelling
functional
analysis
validation of
predictions
in the lab